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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/ commit 2d4c604c2e76baaf744748be3d56e5504a0184b7 |
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added:
swift.xml test-data/datain.21 test-data/map.21 test-data/pedin.21 |
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| diff -r 000000000000 -r 0802a40af216 swift.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/swift.xml Sat Dec 09 17:37:03 2017 -0500 |
| [ |
| @@ -0,0 +1,135 @@ +<tool id="swiftlink" name="Swiftlink" version="@VERSION@.0" > + <description>Parallel MCMC Linkage Analysis</description> + <macros> + <token name="@VERSION@">1.0</token> + <xml name="test_inputs" > + <param name="inp_ped" value="pedin.21" /> + <param name="inp_dat" value="datain.21" /> + <param name="inp_map" value="map.21" /> + </xml> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">swiftlink</requirement> + <requirement type="package" version="2017.3">linkage2allegro</requirement> + </requirements> + <!-- <version_command></version_command> Note: a version is never output by the program... --> + <command detect_errors='exit_code'><![CDATA[ +swiftlink + -p '${inp_ped}' + -m '${inp_map}' + -d '${inp_dat}' + ${misc.X} + ${misc.a} + -q ${misc.q} + -c \${GALAXY_SLOTS:-3} + -i ${mcmc.i} + -b ${mcmc.b} + -s ${mcmc.s} + -x ${mcmc.x} + -l ${mcmc.l} + -n ${mcmc.n} + -R ${mcmc.R} + +#if $misc.r + -r '${misc.r}' +#end if + +#if $elod_opts.e == 'yes': ## 'true' / 'false' as opt values parse badly + -e + -f $elod_opts.f + -w $elod_opts.w + -k '$elod_opts.k' + -u $elod_opts.u 2> ${out_elod} ## stderr and stdout switched for some reason... +#else + -o swiftlink.out + && linkage2allegro '${inp_ped}' '${inp_map}' swiftlink -l swiftlink.out + && mv linkage.allegro_lod '${out_fparam}' +#end if + + ]]> + </command> + + <inputs> + <param name="inp_ped" type="data" format="linkage_pedin" label="Pedigree" /> + <param name="inp_dat" type="data" format="linkage_recomb" label="Recombination Freqs." /> + <param name="inp_map" type="data" format="linkage_map" label="Marker Positions" /> + + <conditional name="elod_opts" > + <param argument="-e" type="select" label="Calculate Expected LOD scores from pedigree only."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes" > + <param name="f" argument="-f" type="float" min="0" max="0.99" value="0.0001" label="Frequency" /> + <param name="w" argument="-w" type="float" min="0" max="1" value="0.5" label="Seperation" /> + <param name="k" argument="-k" type="text" value="0.00,0.00,1.00" label="Penetrance List" /> + <param name="u" argument="-u" type="integer" min="1" value="1000000" label="Replicates" /> + </when> + <when value="no" ></when> + </conditional> + + <section name="mcmc" title="Marko Chain Monte Carlo (MCMC) Options" expanded="false" > + <param argument="-i" type="integer" min="1" value="50000" label="Iterations" /> + <param argument="-b" type="integer" min="1" value="50000" label="Burn-ins" /> + <param argument="-s" type="integer" min="1" value="1000" label="Sequential Imputation" /> + <param argument="-x" type="integer" min="1" value="10" label="Scoring Period" /> + <param argument="-n" type="integer" min="1" value="5" label="Lod Scores" /> + <param argument="-R" type="integer" min="1" value="1" label="Runs" /> + <param argument="-l" type="float" min="0" max="1" value="0.5" label="L-Sampler Probability" /> + </section> + + <section name="misc" title="Miscellaneous" expanded="true" > + <param argument="-X" type="boolean" truevalue="-X" falsevalue="" value="false" label="X-linked"/> + <param argument="-a" type="boolean" truevalue="-a" falsevalue="" value="false" label="Affecteds only"/> + <param argument="-q" type="integer" min="1" value="1000000" label="Peel-sequence Iterator"/> + <param argument="-r" type="data" format="txt" label="Random seeds (single-column)" optional="true" /> + </section> + </inputs> + + <outputs> + <data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: MPT Linkage File" > + <filter>elod_opts['e'] == "no"</filter> + </data> + <data name="out_elod" format="txt" label="${tool.name} on ${on_string}: Elod score" > + <filter>elod_opts['e'] == "yes"</filter> + </data> + </outputs> + + <tests> + <test> + <expand macro="test_inputs" /> + + <param name="b" value="1000" /> + <param name="i" value="2000" /> + <param name="x" value="150" /> + <param name="e" value="yes" /> + <param name="u" value="1000" /> + + <output name="out_elod" > + <assert_contents> + <has_text_matching expression='sex-linked = false' /> + <has_text_matching expression='Total\s+\|\s+\d+\.\d+\s*' /> + </assert_contents> + </output> + </test> + <test> + <expand macro="test_inputs" /> + + <param name="b" value="5000" /> + <param name="i" value="100" /> + <param name="x" value="100" /> + + <output name="out_fparam" > + <assert_contents> + <has_text_matching expression="(\s+-?\d+\.\d+){4}\s+rs468601" /> + </assert_contents> + </output> + </test> + </tests> + <help> +SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees. The current version of SwiftLink only supports SNP markers. + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts704</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 0802a40af216 test-data/datain.21 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datain.21 Sat Dec 09 17:37:03 2017 -0500 |
| b |
| b'@@ -0,0 +1,1172 @@\n+582 0 0 5\n+ 0 0.0 0.0 0 \n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582\n+1 2 \t# TRAIT\n+ 0.9999 0.0001\n+ 1\n+ 0.000 0.000 1.000\n+3 2 \t# rs1296971\n+ 0.4583 0.5417\n+3 2 \t# rs468601\n+ 0.1356 0.8644\n+3 2 \t# rs2821973\n+ 0.4083 0.5917\n+3 2 \t# rs1929150\n+ 0.3559 0.6441\n+3 2 \t# rs2822124\n+ 0.4407 0.5593\n+3 2 \t# rs2775054\n+ 0.2583 0.7417\n+3 2 \t# rs7276618\n+ 0.4167 0.5833\n+3 2 \t# rs392812\n+ 0.1000 0.9000\n+3 2 \t# rs2822368\n+ 0.2833 0.7167\n+3 2 \t# rs6516610\n+ 0.3167 0.6833\n+3 2 \t# rs447455\n+ 0.2000 0.8000\n+3 2 \t# rs437521\n+ 0.1667 0.8333\n+3 2 \t# rs2822554\n+ 0.1417 0.8583\n+3 2 \t# rs2822572\n+ 0.1000 0.9000\n+3 2 \t# rs13050350\n+ 0.3167 0.6833\n+3 2 \t# rs2142236\n+ 0.0667 0.9333\n+3 2 \t# rs2822677\n+ 0.0508 0.9492\n+3 2 \t# rs2822696\n+ 0.0833 0.9167\n+3 2 \t# rs376635\n+ 0.4500 0.5500\n+3 2 \t# rs2822765\n+ 0.4333 0.5667\n+3 2 \t# rs2822780\n+ 0.1667 0.8333\n+3 2 \t# rs465340\n+ 0.4917 0.5083\n+3 2 \t# rs1888398\n+ 0.2250 0.7750\n+3 2 \t# rs458052\n+ 0.3333 0.6667\n+3 2 \t# rs2822907\n+ 0.3250 0.6750\n+3 2 \t# rs8129531\n+ 0.2333 0.7667\n+3 2 \t# rs12053660\n+ 0.1500 0.8500\n+3 2 \t# rs1883003\n+ 0.2750 0.7250\n+3 2 \t# rs2822974\n+ 0.4833 0.5167\n+3 2 \t# rs11088231\n+ 0.1667 0.8333\n+3 2 \t# rs2205239\n+ 0.4250 0.5750\n+3 2 \t# rs2823045\n+ 0.2417 0.7583\n+3 2 \t# rs926164\n+ 0.2750 0.7250\n+3 2 \t# rs2823139\n+ 0.2417 0.7583\n+3 2 \t# rs2823161\n+ 0.3667 0.6333\n+3 2 \t# rs2823194\n+ 0.0750 0.9250\n+3 2 \t# rs2049882\n+ 0.0917 0.9083\n+3 2 \t# rs1736148\n+ 0.4417 0.5583\n+3 2 \t# rs2823301\n+ 0.2583 0.7417\n+3 2 \t# rs6517467\n+ 0.2333 0.7667\n+3 2 \t# rs2064051\n+ 0.2333 0.7667\n+3 2 \t# rs9974915\n+ 0.1000 0.9000\n+3 2 \t# rs2823400\n+ 0.3583 0.6417\n+3 2 \t# rs726634\n+ 0.3167 0.6833\n+3 2 \t# rs7283707\n+ 0.1083 0.8917\n+3 2 \t# rs7283161\n+ 0.4333 0.5667\n+3 2 \t# rs9982633\n+ 0.2500 0.7500\n+3 2 \t# rs2823621\n+ 0.4333 0.5667\n+3 '..b' 0.001712 0.001575 0.000512 0.000567 0.000586 0.001449 0.000862 0.001286 0.000506 0.000518 0.000545 0.001830 0.000665 0.000949 0.001156 0.001236 0.000501 0.000613 0.000572 0.000545 0.000695 0.000524 0.000578 0.000534 0.000970 0.000525 0.000634 0.000567 0.000523 0.000509 0.002036 0.001219 0.001222 0.002258 0.001873 0.001112 0.000799 0.002594 0.000695 0.000502 0.002240 0.000776 0.000534 0.000528 0.002549 0.000504 0.000538 0.001636 0.000791 0.000812 0.001350 0.000502 0.004374 0.000534 0.000518 0.000588 0.000535 0.000754 0.000555 0.001752 0.004448 0.000885 0.001773 0.000566 0.001217 0.000518 0.000732 0.000922 0.000684 0.000503 0.000685 0.000567 0.000543 0.000506 0.000527 0.001806 0.001391 0.000630 0.000505 0.001327 0.000513 0.000664 0.000529 0.000621 0.001258 0.001421 0.000511 0.002351 0.000501 0.000971 0.001581 0.001360 0.000778 0.000590 0.000685 0.001437 0.001497 0.000590 0.000905 0.000541 0.000503 0.001822 0.000779 0.000877 0.000562 0.000526 0.000625 0.000576 0.000600 0.000633 0.001288 0.001829 0.000504 0.000512 0.001125 0.000553 0.000785 0.000776 0.001828 0.000502 0.001045 0.001246 0.000698 0.000868 0.000518 0.000547 0.000676 0.000598 0.000596 0.000690 0.001273 0.000516 0.000503 0.000997 0.001706 0.000721 0.000533 0.000588 0.001516 0.000518 0.001056 0.000507 0.000502 0.002850 0.000626 0.000507 0.000568 0.001302 0.000633 0.002292 0.000500 0.002014 0.000533 0.001410 0.000595 0.000706 0.001283 0.000699 0.001022 0.000681 0.001685 0.001932 0.000864 0.001435 0.001734 0.000653 0.000832 0.000743 0.001876 0.000751 0.000520 0.001096 0.000558 0.000740 0.001345 0.000549 0.001962 0.000521 0.001245 0.000516 0.000517 0.002282 0.000511 0.000811 0.000722 0.001754 0.000511 0.000550 0.001908 0.000534 0.001669 0.001935 0.001493 0.000521 0.000733 0.000816 0.001478 0.000626 0.000520 0.000578 0.001743 0.000501 0.001703 0.000526 0.000628 0.000540 0.001511 0.001159 0.000523 0.000984 0.002506 0.000619 0.002135 0.001293 0.000559 0.000509 0.000530 0.000621 0.001215 0.000594 0.000945 0.002575 0.000588 0.000588 0.001190 0.000544 0.001123 0.001036 0.000564 0.000514 0.000816 0.000939 0.001210 0.000698 0.000526 0.001199 0.001589 0.002322 0.000500 0.000600 0.000804 0.001471 0.000520 0.000679 0.000669 0.000976 0.000614 0.000676 0.001038 0.000881 0.000790 0.001515 0.002322 0.000535 0.001803 0.002088 0.000883 0.000826 0.000703 0.000743 0.000651 0.001431 0.000923 0.000535 0.001250 0.000957 0.000697 0.001615 0.000817 0.001998 0.000638 0.000531 0.000910 0.001797 0.000571 0.001722 0.003449 0.001449 0.000801 0.001141 0.000504 0.001250 0.001787 0.000573 0.000845 0.000968 0.005449 0.000563 0.000721 0.001198 0.000552 0.001350 0.001014 0.000675 0.000537 0.000533 0.001793 0.000817 0.000520 0.002322 0.000551 0.000773 0.001852 0.000526 0.001451 0.000606 0.001702 0.000714 0.000602 0.000608 0.001443 0.000767 0.001225 0.000925 0.000505 0.000753 0.001616 0.001311 0.002005 0.001083 0.000615 0.000579 0.000516 0.001166 0.000934 0.001147 0.001770 0.000501 0.000674 0.001566 0.000736 0.000546 0.001212 0.000502 0.001283 0.000777 0.000782 0.000579 0.000977 0.001867 0.000720 0.002157 0.001494 0.002188 0.001952 0.001566 0.000694 0.001341 0.001138 0.000879 0.000570 0.001607 0.000732 0.000613 0.000502 0.000776 0.000990 0.000737 0.000643 0.000579 0.000625 0.000514 0.000962 0.000690 0.002351 0.001055 0.001971 0.000545 0.000640 0.002772 0.000510 0.000516 0.000636 0.000763 0.001327 0.000871 0.001994 0.000702 0.000581 0.000505 0.000585 0.001833 0.001476 0.000813 0.001382 0.001200 0.000533 0.001116 0.001082 0.001198 0.000976 0.000507 0.000527 0.001056 0.003941 0.001371 0.000501 0.000501\n+ 1 2.0 1.0\n' |
| b |
| diff -r 000000000000 -r 0802a40af216 test-data/map.21 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/map.21 Sat Dec 09 17:37:03 2017 -0500 |
| b |
| b'@@ -0,0 +1,582 @@\n+#Chr Genpos Marker Physpos Nr\n+ 21 0.70496629 rs1296971 13609442 1\n+ 21 0.77494263 rs468601 13769165 2\n+ 21 0.85010932 rs2821973 13899316 3\n+ 21 1.01291458 rs1929150 14051249 4\n+ 21 1.07552959 rs2822124 14088675 5\n+ 21 1.16577144 rs2775054 14121682 6\n+ 21 1.34457997 rs7276618 14197852 7\n+ 21 1.44169062 rs392812 14252347 8\n+ 21 1.60661592 rs2822368 14311592 9\n+ 21 1.73090413 rs6516610 14385827 10\n+ 21 1.78470487 rs447455 14502698 11\n+ 21 1.89865013 rs437521 14513560 12\n+ 21 1.95928889 rs2822554 14585162 13\n+ 21 2.00968909 rs2822572 14618073 14\n+ 21 2.09569547 rs13050350 14653413 15\n+ 21 2.14611500 rs2142236 14748155 16\n+ 21 2.30459845 rs2822677 14767432 17\n+ 21 2.35507107 rs2822696 14783326 18\n+ 21 2.49458320 rs376635 14788185 19\n+ 21 2.54981913 rs2822765 14843387 20\n+ 21 2.69205997 rs2822780 14875052 21\n+ 21 2.74542953 rs465340 14884525 22\n+ 21 2.80926447 rs1888398 14981052 23\n+ 21 2.86888387 rs458052 15013563 24\n+ 21 2.93942924 rs2822907 15057767 25\n+ 21 2.99612354 rs8129531 15061195 26\n+ 21 3.15050759 rs12053660 15067326 27\n+ 21 3.48398239 rs1883003 15147347 28\n+ 21 3.62725156 rs2822974 15185311 29\n+ 21 3.69755891 rs11088231 15247441 30\n+ 21 3.83233721 rs2205239 15365789 31\n+ 21 4.03050303 rs2823045 15382630 32\n+ 21 4.11519240 rs926164 15435118 33\n+ 21 4.17500340 rs2823139 15498654 34\n+ 21 4.22973041 rs2823161 15515055 35\n+ 21 4.31848934 rs2823194 15568649 36\n+ 21 4.53372425 rs2049882 15633372 37\n+ 21 4.62105207 rs1736148 15735083 38\n+ 21 4.80636119 rs2823301 15780469 39\n+ 21 4.88644465 rs6517467 15806025 40\n+ 21 4.96357163 rs2064051 15860950 41\n+ 21 5.04209154 rs9974915 15879012 42\n+ 21 5.09648993 rs2823400 15922925 43\n+ 21 5.28044978 rs726634 15952748 44\n+ 21 5.33607360 rs7283707 16048865 45\n+ 21 5.52020653 rs7283161 16247081 46\n+ 21 5.60568022 rs9982633 16341775 47\n+ 21 5.70676016 rs2823621 16453860 48\n+ 21 5.81125072 rs2051347 16485140 49\n+ 21 5.90261793 rs2823702 16551609 50\n+ 21 6.11205825 rs189457 16586547 51\n+ 21 6.19207523 rs2823748 16597546 52\n+ 21 6.50682420 rs2849869 16651064 53\n+ 21 6.65214516 rs1667568 16668191 54\n+ 21 6.71981324 rs171267 16678743 55\n+ 21 6.82475021 rs11911987 16722383 56\n+ 21 7.39610093 rs2823881 16856068 57\n+ 21 7.50376261 rs2823912 16917157 58\n+ 21 7.63480472 rs2032287 16930320 59\n+ 21 7.84039602 rs4818278 16998424 60\n+ 21 8.04214302 rs11700643 17038979 61\n+ 21 8.22354552 rs418989 17157305 62\n+ 21 8.36525000 rs4818307 17217065 63\n+ 21 8.45433331 rs11701390 17283040 64\n+ 21 8.51634344 rs2824192 17343668 65\n+ 21 8.67406372 rs2824231 17392912 66\n+ 21 8.77025758 rs1501813 17554542 67\n+ 21 8.82932246 rs2824273 17561990 68\n+ 21 8.88853994 rs2824282 17645542 69\n+ 21 9.03723097 rs4536738 17662409 70\n+ 21 9.09085593 rs2824292 17709047 71\n+ 21 9.16009205 rs208885 17730794 72\n+ 21 9.53979856 rs2849886 17786057 73\n+ 21 9.59018991 rs764657 17848524 74\n+ 21 9.69271956 rs9977638 17890191 75\n+ 21 9.85245414 rs2824435 17966268 76\n+ 21 10.08197365 rs243570 18050577 77\n+ 21 10.35520368 rs243587 18076288 78\n+ 21 10.47428859 rs243619 18133788 79\n+ 21 10.53651389 rs2824560 18225088 80\n+ 21 10.61943861 rs200801 18255517 81\n+ 21 10.67244619 rs157740 18325093 '..b'42270504 498\n+ 21 53.47724640 rs7275759 42315905 499\n+ 21 53.63914552 rs220229 42321866 500\n+ 21 53.77042330 rs220245 42332241 501\n+ 21 53.97131367 rs150796 42336818 502\n+ 21 54.07972089 rs2839461 42374420 503\n+ 21 54.14129822 rs220109 42395418 504\n+ 21 54.19927272 rs13051533 42418558 505\n+ 21 54.25090134 rs1563357 42429404 506\n+ 21 54.36764383 rs4148105 42517078 507\n+ 21 54.46110749 rs7281345 42548051 508\n+ 21 54.57594042 rs7275482 42582769 509\n+ 21 54.75328382 rs2236705 42605897 510\n+ 21 54.80343867 rs11701981 42654887 511\n+ 21 54.87092093 rs755946 42668234 512\n+ 21 55.02776386 rs3814900 42682895 513\n+ 21 55.10145520 rs9784215 42696805 514\n+ 21 55.15610210 rs8130358 42748917 515\n+ 21 55.27740762 rs2839536 42778956 516\n+ 21 55.32767760 rs228082 42840195 517\n+ 21 55.45611008 rs11701162 42899212 518\n+ 21 55.53384184 rs380422 42906052 519\n+ 21 55.61211206 rs2138327 42959024 520\n+ 21 55.67004843 rs2839576 43013026 521\n+ 21 55.76785187 rs7279886 43042997 522\n+ 21 55.95494040 rs2839585 43110613 523\n+ 21 56.02694911 rs1672133 43280210 524\n+ 21 56.24316412 rs2027745 43381089 525\n+ 21 56.39274380 rs879648 43458474 526\n+ 21 56.61198420 rs2839641 43472790 527\n+ 21 56.80752447 rs762391 43540212 528\n+ 21 56.96435208 rs638268 43562311 529\n+ 21 57.03380458 rs566038 43567174 530\n+ 21 57.16806420 rs681210 43603771 531\n+ 21 57.28200405 rs672163 43647907 532\n+ 21 57.36993361 rs657918 43655383 533\n+ 21 57.42698281 rs162382 43708680 534\n+ 21 57.58789627 rs1107204 43962546 535\n+ 21 57.66113088 rs4819314 44024166 536\n+ 21 57.72246792 rs2838429 44150344 537\n+ 21 57.77269640 rs3737358 44215567 538\n+ 21 57.85034353 rs2277806 44334078 539\n+ 21 57.94941280 rs743479 44436378 540\n+ 21 58.02316868 rs2070561 44482398 541\n+ 21 58.08753427 rs2018054 44528088 542\n+ 21 58.14545131 rs2256817 44539814 543\n+ 21 58.20798405 rs2070572 44582333 544\n+ 21 58.25939371 rs2838551 44588825 545\n+ 21 58.35567202 rs2003775 44678814 546\n+ 21 58.42472189 rs2838567 44718335 547\n+ 21 58.66040246 rs8134902 44798306 548\n+ 21 58.76599607 rs11702525 44843611 549\n+ 21 58.96345573 rs13051885 44869053 550\n+ 21 59.01797405 rs1107121 44951977 551\n+ 21 59.08201090 rs235380 44970169 552\n+ 21 59.35995642 rs2838674 45005437 553\n+ 21 59.41099672 rs2838704 45088803 554\n+ 21 59.46261324 rs3788142 45141068 555\n+ 21 59.52627192 rs760462 45152527 556\n+ 21 59.60265124 rs3788151 45161993 557\n+ 21 59.73554629 rs2838738 45168854 558\n+ 21 59.82267904 rs7283236 45177740 559\n+ 21 60.02251199 rs2838753 45266375 560\n+ 21 60.09274976 rs2838760 45305933 561\n+ 21 60.15089724 rs2838763 45312330 562\n+ 21 60.20144195 rs7281416 45430267 563\n+ 21 60.26001146 rs10098 45539973 564\n+ 21 60.44360603 rs914237 45574146 565\n+ 21 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